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(-) Description

Title :  LATERAL OPENING OF A TRANSLOCON UPON ENTRY OF PROTEIN SUGGESTS THE MECHANISM OF INSERTION INTO MEMBRANES
 
Authors :  P. F. Egea, R. M. Stroud, Center For Structures Of Membrane Protei
Date :  26 Apr 10  (Deposition) - 06 Oct 10  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Transport, Membrane Protein Complex, Preprotein Translocase, Membrane Insertion, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. F. Egea, R. M. Stroud
Lateral Opening Of A Translocon Upon Entry Of Protein Suggests The Mechanism Of Insertion Into Membranes.
Proc. Natl. Acad. Sci. Usa V. 107 17182 2010
PubMed-ID: 20855604  |  Reference-DOI: 10.1073/PNAS.1012556107

(-) Compounds

Molecule 1 - PREPROTEIN TRANSLOCASE SUBUNIT SECY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: BL21(AI)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SECY
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA HOMOLOG
 
Molecule 2 - PREPROTEIN TRANSLOCASE SUBUNIT SECE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: BL21(AI)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SECE
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT HOMOLOG

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3MP7)

(-) Sites  (0, 0)

(no "Site" information available for 3MP7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MP7)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Gly A:226 -Asp A:227
2Trp A:229 -Gly A:230
3Tyr A:233 -Arg A:234
4Arg A:234 -Gly A:235
5Gly A:236 -Ser A:237
6Ser A:237 -Ala A:238
7Ala A:468 -Gly A:469
8Lys B:22 -Lys B:23
9Pro B:24 -Asn B:25

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MP7)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SECY_1PS00755 Protein secY signature 1.SECY_PYRFU72-91  1A:72-90
2SECY_2PS00756 Protein secY signature 2.SECY_PYRFU163-180  1A:163-180

(-) Exons   (0, 0)

(no "Exon" information available for 3MP7)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:387
 aligned with SECY_PYRFU | Q8U019 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    468  
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465  |  
           SECY_PYRFU    26 LRERFMWTGVALILYYVLAEIPVYGIPERIQDYFQFLRVVLAGRNGSILTLGIGPIVTAGIILQLLVGSEIIKLDLANPEDRRFYQALQRVFSVFMCFFEAAVWILGGAFGRVGVDVTYAIAVLMILQLAMGGIVLIILDELVSKWGIGSGISLFIAAGVSQTILTRSLNPLTDPNIIDPLTGQPAIVGAIPYFIQHILKGDLWGAIYRGGSAPDMLSVVATIVVFFIVVYFESMRVEIPLGYRGVTVRGSYPIRFLYVSNIPIILTFALYANIQLWARVLDRLGHPWLGRFDPTTGSPISGFVLYVIPPRNIFSVIDNPVRAIVYLILTVIFSLLFGYLWVELTGLDARSIARQLQRAGLQIPGFRRDPRTLEKVLQRYIPYVTFWGSLTVALIAVLADFLGALGTGTGILLTVGILYRFYEEIAREQITEMFPALRKLFGA--   -
               SCOP domains d3mp7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------Plug_translocon-3mp7A01 A:38-71   SecY-3mp7A02 A:72-4                       48                                                                                                                                                                                                                                                                                                                                             ---------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh...............................hhhhhhhhhhh..-----------------------hhhhhhhhhhhhhhhhhhh......------.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......---.........hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh....------------.........hhhhhhhhhhhhhhhhhhhhhhh...................hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..--------.............------.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------SECY_1  PDB: A:72-90-----------------------------------------------------------------------SECY_2            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mp7 A  26 LRERFMWTGVALILYYVLAEIPVYGIPERIQDYFQFLRVVLAGRNGSILTLGIGPIVTAGIILQL-----------------------QRVFSVFMCFFEAAVWILGGAFGRV------AIAVLMILQLAMGGIVLIILDELVSKWGIGSGISLFIAAGVSQTILTRSLNPLTDPN---PLTGQPAIVGAIPYFIQHILKGDLWGAIYRGGSAPDMLSVVATIVVFFIVVYFESMRVEI------------YPIRFLYVSNIPIILTFALYANIQLWARVLDRLGHPWLGRFDPTTGSPISGFVLYVIPPRNIFSVIDNPVRAIVYLILTVIFSLLFGYLWVELTGLDARSIAR--------IPGFRRDPRTLEK------PYVTFWGSLTVALIAVLADFLGALGTGTGILLTVGILYRFYEEIAREQITEMFPALRKLFGAGT 470
                                    35        45        55        65        75        85    |    -         -       115       125       135  |    145       155       165       175       185       195     | 205       215       225       235       245       255        |-         - |     285       295       305       315       325       335       345       355       365       375   |     -  |    395    |    - |     415       425       435       445       455       465     
                                                                                           90                     114                     138    145                                                     201 205                                                        264          277                                                                                                   379      388         400    407                                                               


Chain B from PDB  Type:PROTEIN  Length:54
 aligned with SECE_PYRFU | Q8TZK2 from UniProtKB/Swiss-Prot  Length:61

    Alignment length:54
                                    17        27        37        47        57    
           SECE_PYRFU     8 IRHFWKESRRAFLVTKKPNWATYKRAAKITGLGIILIGLIGMLIRIVGILILGG  61
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 3mp7 B   7 IRHFWKESRRAFLVTKKPNWATYKRAAKITGLGIILIGLIGMLIRIVGILILGG  61
                                    16        26|       37        47        57    
                                              26|                                 
                                               28
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MP7)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Plug_translocon] (6)
(-)
Clan: no clan defined [family: SecY] (6)

(-) Gene Ontology  (11, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SECY_PYRFU | Q8U019)
biological process
    GO:0065002    intracellular protein transmembrane transport    The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
    GO:0006605    protein targeting    The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (SECE_PYRFU | Q8TZK2)
molecular function
    GO:0015450    P-P-bond-hydrolysis-driven protein transmembrane transporter activity    Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated.
    GO:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0065002    intracellular protein transmembrane transport    The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0006605    protein targeting    The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  Cis Peptide Bonds
    Ala A:468 - Gly A:469   [ RasMol ]  
    Arg A:234 - Gly A:235   [ RasMol ]  
    Gly A:226 - Asp A:227   [ RasMol ]  
    Gly A:236 - Ser A:237   [ RasMol ]  
    Lys B:22 - Lys B:23   [ RasMol ]  
    Pro B:24 - Asn B:25   [ RasMol ]  
    Ser A:237 - Ala A:238   [ RasMol ]  
    Trp A:229 - Gly A:230   [ RasMol ]  
    Tyr A:233 - Arg A:234   [ RasMol ]  
 

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  SECY_PYRFU | Q8U019
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1rh5
2yxq
2yxr
2zjs
3dkn RELATED ID: CSMP-1154S RELATED DB: TARGETTRACK RELATED ID: CSMP-1152S RELATED DB: TARGETTRACK